I wouldn't be surprised if an AS Mac Pro didn't support traditional graphics cards, and Apple released their own accelerators similar to the Afterburner card. That way they can optimise them to suit their apps/workflows/partners.
Essentially go back to the Mac Pro 2013 baseline design? Errr, probably not.
First, the Afterburner card fits into any of the 3 x16 slots in a Mac Pro 2019. If it fits into a "normal" slot, so can all of the other cards that fit into a normal slot. ( also need drivers. Apple isn't blocking drivers that follow their rules and roadmaps. ). The Afterburner card does not preclude in any way some 3rd party FPGA card from being inserted into the MP 2019. If there was a driver for it, it would work.
Afterburner doesn't work all that great as an "accelerator" in a external PCI-e box ( eGPU) whereas can add horsepower to lots of x86 Mac laptops and iMacs with a driver supported , off-the-shelf card. If the tansitor budget gets big enough "ProRes RAW" fixed function logic could easier find its way into the Apple Silicon in 1-2 future generations. ( Apple specific stuff is just as least as likely to land inside a future SoC than outside. Outside in Afterburner made lots of sense because ProRes RAW was entangled during the development with Red Patent legal drama. FPGA allowed them large flexibility in dealing with whatever the outcome was on the short-intermediate term. )
Second, simply just go back to the intro for the MP 2019 where Apple bragged about :
i. having the most Pro Tools HDX cards in a single box/system.
ii. the M.2 SSD PCI-e cards you could put into the system.
Can try to paint this into just simply being a Final Cut Pro box , but that isn't necessarily the majority of the target market. Apple is only likely going to to 10GbE. There are 40-100+ GbE networks out there to interface with.
Some folks have relatively extremely fast storage I/O needs.
It isn't only about GPU cards. Apple is extremely unlikely to "cover' the whole GPU performance range. They are even more unlikely going to try to cover the entire PCI-e add-in-card landscape.
Once there are 1-2 other "normal" PCI-e slots presents it isn't a huge leap to have a MPX enabled slot there in addition. One MPX bay ( with two slots; one with an MPX connector ) and perhaps one other "normal" single width slot would cut the system height ( in tower format ) down within the ball park of half ( if prune a small bit out the CPU area. ) . Would have at least 3 slots and at least one double wide one. All need is the optional power connectors (which doesn't cost much in terms of design) and to enable the GPU drivers ( which is the bigger missing piece at the moment).
For a full (present) height of the Mac Pro the bulks of the height is the standard slots. If keeping the height might as well keep the slots.
The major difference with Apple Silicon is two fold.
One, Apple security model for the kernel has changes and right now it is simpler if only Apple GPU drivers are in a Apple kernel. ( if Apple doesn't start to open door at WWDC 2021 with macOS 12 kernel and IO driver stack changes then can start to put on the "doom and gloom" for 3rd party GPUs. ).
Two, Apple is trying to get folks to highly optimize for their specific GPUs. That is much easier to do when there are no other options on the table.
Once Apple gets to point of 90+ % of all new Macs sold have Apple embedded GPUs in them the inertia will take care of #2. Apple won't have to "herd" folks in that direction; market forces will do it. Of the gate though the installed base of Mac on x86 with Intel/AMD GPUs greatly outnumbered the M1 install base.
Apple probably does want to wipe all 3rd party GPUs from inside all of the laptop line up and the lower part of the desktop line up. But it seems doubtful that they will want to go toe-to-toe with the top end of the discrete card market. This 6800Xt shows some 2x improvements they'd have to cover. Today there are some rumors floating around how the top end Navi 31 will be more than a 2x improvement over that in late 2022. 400W budget and $2,000-6,000 money budget is going to 'buy' bleeding edge performance that Apple would 'have to' cover is artificially block all 3rd party options.
I suspect Apple just wants to keep the profitable GPU part and leave the low volume parts to other player. ( and likewise apple probably won't go into the ultimate "core count" war with AMD/Intel/Ampere etc. on CPU cores either with the Mac Pro).